1990LS400 is the most knowledgeable on this subject IMO. There was another guy that gave good instructions though.
This is the wiring I did, I used a 6 pin harness for everything but the speakers wires for easy servicing, for the speakers I used an RCA cable that I've cut in half and soldered to the 8 wires (make sure you respect polarity) on the B plug
Battery 12v (B+ Cyan_Blue/Yellow on C1)
Accessory (ACC grey on C6)
Ground (GND2 brown on C14)
Power Antenna (ANT+ Black/Red on C12)
Amp remote (AMP+ Pink/Cyan on B11)
FL Speaker (+) BLACK (B2) to RCA
FL Speaker (-) WHITE (B7) to RCA
FR Speaker (+) WHITE (B1) to RCA
FR Speaker (-) RED (B6) to RCA
RL Speaker (+) RED (B5) to RCA
RL Speaker (-) GREEN (B14) to RCA
RR Speaker (+) YELLOW (B4) to RCA
RR Speaker (-) GREEN (B13) to RCA
Wait... where's the sub signal??? There's none, everything is happening at the amp.
The amp is using the signal from FL,FR,RL,RR and feed the sub with it, but the way it work is that it high pass the signal for the doors (~100Hz) and low pass the signal for the sub.
When I started the system after replacing the HU in mine, I didn't have any sub. Went into my deck settings and removed the HPF (High pass filter) that was set at 120Hz. Bam! I can hear the sub, go into my EQ and boost 60Hz and the car is shaking.
Basically all the bass knob on the deck was doing is to boost or lower the lower frequency and only the sub is affected because of the LPF and HPF that is set in the amp.
Now for those who want more punch out of their system, you need to bypass the the nak amp before replacing speakers in your doors. Since there's an HPF set in the Nak amp, even if you put 8" in your doors you wont get much more midbass out of them.
If you already did this and you can't hear your sub, here's some things to check. First make sure your RCA output are set to fullrange (no HPF) in your headunit. Some HU will automatically set an HPF if the sub is enable so check that too.
Next, check that you respected the polarity on all RCA, if you have one inverted it will cancel out (phase inverted) the sub since all channels go to one speaker. To see if that's your problem, simply set the balance to one side and do the same for the fader so that only one speaker play. Crank the lowest EQ settings you have (ideally 80Hz or less) and you should hear the sub.
HTH